5RC5

PanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library F06b


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62900.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
1.8834.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.234α = 90
b = 73.008β = 109.17
c = 52.296γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.827MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.0342.7698.50.0820.0890.99812.46.76814945518.748
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.241.320.920.8010.8690.7712.216.0414538

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.0342.76149455787398.380.16620.165220.16618RANDOM13.732
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.18-0.370.150.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.028
r_dihedral_angle_4_deg16.65
r_dihedral_angle_3_deg11.301
r_dihedral_angle_1_deg6.498
r_angle_refined_deg1.836
r_mcangle_it1.614
r_angle_other_deg1.605
r_mcbond_it1.11
r_mcbond_other1.099
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.028
r_dihedral_angle_4_deg16.65
r_dihedral_angle_3_deg11.301
r_dihedral_angle_1_deg6.498
r_angle_refined_deg1.836
r_mcangle_it1.614
r_angle_other_deg1.605
r_mcbond_it1.11
r_mcbond_other1.099
r_chiral_restr0.094
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2371
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms72

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
PHENIXrefinement